#! /usr/bin/python from cctbx import uctbx, sgtbx import string, math from pymol.cgo import * from pymol import cmd from all_axes import * from Numeric import * def read_symop_dat(sg_input=None): linecounter = 0 axes = {} file = file('symop_axes.dat','r') lines = file.readlines() num_lines=len(lines) #for line in lines: #for line in file.readlines(): while (1): line = lines[linecounter] if line[0] != '#' and line[0] != '': #print linecounter, line try: #(sgsgnum,num_ax,sg) = line.split(None,3) (sg,sgnum,num_ax,junk) = line.split(None,3) except: print linecounter,line num_ax = string.atoi(num_ax) axes[sg] = [] for i in range(num_ax): linecounter = linecounter + 1 #sg_line = file.readline() sg_line = lines[linecounter].split() tmp_dict = {} #print linecounter, sg_line tmp_dict['start'] = [string.atof(j) for j in sg_line[0:3]] tmp_dict['end'] = [string.atof(j) for j in sg_line[3:6]] tmp_dict['symb'] = sg_line[6] #tmp_dict['type'] = sg_line[7] axes[sg].append(tmp_dict) linecounter = linecounter + 1 if linecounter >= num_lines: break if sg_input != None: sg_input = sg_input.upper() #for i in range(len(axes[sg_input])): # print axes[sg_input][i] return axes[sg_input] else: return axes def draw_symbol(start,end,symb,color,radius=0.2): degtorad = math.pi/180. costhirty = math.cos(30.0*degtorad) sinthirty = math.sin(30.0*degtorad) symb_obj = [] if symb == '2' or symb == '2^1': pass elif symb == '3' or symb == '3^1' or symb == '3^2': symb_obj = [ BEGIN, TRIANGLES, COLOR ] + color symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([radius, 0, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([-radius*sinthirty, radius*costhirty, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([-radius*sinthirty, -radius*costhirty, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([radius, 0, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([-radius*sinthirty, radius*costhirty, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([-radius*sinthirty, -radius*costhirty, 0]))[0].tolist() symb_obj.append(END) elif symb == '4' or symb == '4^1' or symb == '4^2' or symb == '4^3': symb_obj = [ BEGIN, TRIANGLES, COLOR ] + color symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([-radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([-radius, -radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([radius, -radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([start]) + array([-radius, -radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([-radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([-radius, -radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([radius, radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([radius, -radius, 0]))[0].tolist() symb_obj.append(VERTEX) symb_obj = symb_obj + (array([end]) + array([-radius, -radius, 0]))[0].tolist() symb_obj.append(END) elif symb == '6' or symb == '6^1' or symb == '6^2' or symb == '6^3' or symb == '6^4' or symb == '6^5': pass return symb_obj def draw_symops(cell_param_list,sg,radius=0.2): """ From pymol issue the "run draw_symops.py" command to load the script, then issue the "draw_symops((cell_param_list),,)" command to actually run it and create the cgo object. E.g. "draw_symops((45.2,45.2,70.8,90.,90.,120.),'p3121',0.5)" to generate the symmetry operators for this trigonal space group "p 31 2 1" The different axis types appear as different objects on the PyMOL menu so they can be turned on and off individually. """ U=uctbx.unit_cell((cell_param_list)) #rotation axes # "2" "yellow", # "3" "orange", # "4" "mauve", # "6" "purple", #screw axes (all sub_1 axes are green) # "21" "green", # "31" "green", # "32" "lime", # "41" "green", # "42" "cyan", # "43" "iceblue", # "61" "green", # "62" "silver", # "63" "cyan", # "64" "iceblue", # "65" "blue", color = { "2" : [1.0, 1.0, 0.0], "3" : [1.0, 0.5, 0.0], "4" : [1.0, 0.5, 1.0], "6" : [1.0, 0.0, 1.0], "2^1" : [0.0, 1.0, 0.0], "3^1" : [0.0, 1.0, 0.0], "3^2" : [0.5, 1.0, 0.5], "4^1" : [0.0, 1.0, 0.0], "4^2" : [0.0, 1.0, 1.0], "4^3" : [0.5, 0.5, 1.0], "6^1" : [0.0, 1.0, 0.0], "6^2" : [0.8, 0.8, 0.8], "6^3" : [0.0, 1.0, 1.0], "6^4" : [0.5, 0.5, 1.0], "6^5" : [0.0, 0.0, 1.0], } sg = sg.upper() symop_axes = read_symop_dat(sg) #symop_axes = get_all_axes(sg) #CYLINDER = 'CYLINDER' ax_obj = {} #vert_obj = [] for i in range(len(symop_axes)): start = map(None,U.orthogonalize(symop_axes[i]['start'])) end = map(None,U.orthogonalize(symop_axes[i]['end'])) color_ax = color[symop_axes[i]['symb']] symb_ax = symop_axes[i]['symb'] if ax_obj.has_key(symb_ax): ax_obj[symb_ax].append(CYLINDER) else: ax_obj[symb_ax] = [CYLINDER] ax_obj[symb_ax] = ax_obj[symb_ax] + start + end + [radius] ax_obj[symb_ax] = ax_obj[symb_ax] + color[symb_ax] + color[symb_ax] ax_obj[symb_ax] = ax_obj[symb_ax] + draw_symbol(start,end,symb_ax,color[symb_ax],radius*3.) for key in ax_obj.keys(): name=sg + "_" + key cmd.load_cgo(ax_obj[key],name) #return ax_obj cmd.extend("draw_symops",draw_symops)